Cytokines regulate cellular growth and differentiation, along with immune and inflammatory responses. They are critical in the pathogenesis of autoimmune diseases such as rheumatoid arthritis, SLE, IBD, psoriasis, allergy and asthma. Targeting cytokines and cytokine signaling has led to successful new strategies in treating these diseases, underscoring the need to better understand the molecular basis of cytokine action as it relates to the pathogenesis of immune-mediated disease. A critical means by which cytokines exert their effect is activation of receptor-associated Janus kinases, or JAKs, and the activation of a family of transcription factors called STATs; this has been the focus of our work for the last two decades. One important action of cytokines in which STATs play a key role is the differentiation of different subsets of lymphocytes to attain distinct fates, and this too has been a longstanding interest of the lab. The transcription factor STAT5 is fundamental to the mammalian immune system. However, the relationship between its two paralogs, STAT5A and STAT5B, and the extent to which they are functionally distinct, remain uncertain. Using mouse models of paralog deficiency, we demonstrated that they are not equivalent for CD4 'helper' T cells, the principal orchestrators of adaptive immunity. Instead, we found that STAT5B is dominant for both effector and regulatory (Treg) responses and, therefore, uniquely necessary for immunological tolerance. Comparative analysis of genomic distribution and transcriptomic output confirm that STAT5B has far greater impact but, surprisingly, the data point towards asymmetric expression (i.e. paralog dose), rather than distinct functional properties, as the key distinguishing feature. Previously, we demonstrated the importance of Stat3 for Th17 differentiation and, in collaboration with NIH colleagues, showed that this was relevant to the pathogenesis of Hyperimmunoglobulin E or Jobs syndrome. Interleukin-6 (IL-6) and IL-27 both employ Stat1 and Stat3 for signaling. We assessed the relative contributions of STAT1 and STAT3 using genetic models and chromatin immunoprecipitation-sequencing (ChIP-seq) approaches. We found an extensive overlap of the transcriptomes induced by IL-6 and IL-27 and few examples in which the cytokines acted in opposition. Using STAT-deficient cells and T cells from patients with gain-of-function STAT1 mutations, we demonstrated that STAT3 is responsible for the overall transcriptional output driven by both cytokines, whereas STAT1 is the principal driver of specificity. Interleukin-23 (IL-23) is a pro-inflammatory cytokine that also activates STAT3 and is required for the pathogenicity of T helper 17 (Th17) cells. However, the molecular mechanisms governing pathogenicity remain unclear. We identified the transcription factor Blimp-1 (Prdm1) as a key IL-23-induced factor that drives the inflammatory function of Th17 cells. Genome-wide occupancy and overexpression studies in Th17 cells revealed that Blimp-1 co-localized with transcription factors RORgt, STAT3, and p300 at the Il23r, Il17a/f, and Csf2 cytokine loci and enhanced their expression. Blimp-1 also directly bound to and repressed cytokine loci Il2 and Bcl6. Taken together, our results demonstrate that Blimp-1 is an essential transcription factor downstream of IL-23 that acts in concert with RORgt to activate the Th17 inflammatory program. In collaboration, we also identified the kinase DYRK1A as an important regulator of Th17 versus Treg differentiation. IL-9 is an important cytokine that also has important roles in intestinal barrier function. A subset of CD4 T cells that preferentially produce IL-9 are termed Th9 cells. In collaboration, we showed that TL1A potently promotes generation of Th9 cells through an IL-2 and STAT5-dependent mechanism, unlike the TNF-family member OX40, which promotes Th9 through IL-4 and STAT6. A major focus over the past several years has been to approach the issue of helper T cell specification using new genomic tools. A powerful technique has been chromatin immunoprecipitation and massive parallel sequencing (ChIP-seq). We used this technology to map active enhancer elements in T helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the activation of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. More recently, we have used this approach to identify regions of the genome that are subject to intense regulation, so-called stretch or super-enhancers (SEs). We analyzed maps of mouse T-cell SEs as a non-biased means of identifying key regulatory nodes involved in cell specification and found that cytokines and cytokine receptors were the dominant class of genes exhibiting SE architecture in T cells. The locus encoding Bach2, a key negative regulator of effector differentiation, emerged as the most prominent T-cell SE, revealing a network in which SE-associated genes critical for T-cell biology are repressed by BACH2. Disease-associated single-nucleotide polymorphisms for immune-mediated disorders, including rheumatoid arthritis, were highly enriched for T-cell SEs versus typical enhancers or SEs in other cell lineages. Treatment of T cells with the Janus kinase inhibitor tofacitinib disproportionately altered the expression of rheumatoid arthritis risk genes with SE structures. In collaboration, we extended our work on Bach2 to study its role on the differentiation state of CD8 T cells. We found that the TF BACH2 restrains terminal differentiation to enable generation of long-lived memory cells and protective immunity after viral infection. BACH2 was recruited to enhancers, where it limited expression of TCR-driven genes by attenuating the availability of activator protein-1 (AP-1) sites to Jun family signal-dependent TFs. In naive cells, this prevented TCR-driven induction of genes associated with terminal differentiation, but in effector cells reduced expression enabling unrestrained induction of TCR-driven programs. Innate lymphoid cells (ILCs) represent a subset of cells that play key roles in host defense, barrier integrity, and homeostasis and mirror adaptive CD4 T helper (Th) cell subtypes in both usage of effector molecules and transcription factors. To better understand the relationship between ILC subsets and their Th cell counterparts, we measured genome-wide chromatin accessibility. We found that chromatin in proximity to effector genes is selectively accessible in ILCs prior to high-level transcription upon activation. Accessibility of these regions is acquired in a stepwise manner during development and changes little after in vitro or in vivo activation. Conversely, dramatic chromatin remodeling occurs in naive CD4 T cells during Th cell differentiation during parasite infection. This alteration results in a substantial convergence of Th2 cells toward ILC2 regulomes. Our data indicate extensive sharing of regulatory circuitry across the innate and adaptive compartments of the immune system, in spite of their divergent developing pathways. In related work, we investigated the role of EZH2, a component of the Polycomb complex in helper T cells. We found that deletion of Ezh2 in CD4 T cells resulted in reduced numbers of regulatory T cells. We found that both Ezh2-deficient Treg cells and T effector cells were functionally impaired in vivo: Tregs failed to constrain autoimmune colitis, and T effector cells neither provided a protective response in infection nor mediated autoimmune colitis. This year we also reported the development of a new tool for Chip-seq analysis: PAPST, or Peak Assignment and Profile Search Tool.